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Kortemme-Lab / loop_modeling

A loop modeling benchmark capture containing the benchmark dataset and benchmarked protocol captures.
https://kortemmelab.ucsf.edu/benchmarks
MIT License
5 stars 7 forks source link

HETATMs in reference structures #7

Open smlewis opened 7 years ago

smlewis commented 7 years ago

In the 14-17 benchmark, some reference structures (input/structures/14_17_res/rosetta/reference/ folder) have HETATMS:

1r6x 1ra0 1rdq 1s95 2aeb 2b0t 2bwr 2puh 3a3p 3a64 3b40 3cnq 3ea1

These blow up the RMSD step for some ways of calculating RMSD. My use of this benchmark isn't totally "inside" - I'm doing the RMSD in its own separate RosettaScripts step - so it might affect only me. I'm filing the issue because I'm having to remove the heteroatoms to get it to work for my purposes. I can PR fixed structures if it is determined that they are wanted, but I'm not sure that it's relevant for the "official" use of the data.

kalekundert commented 7 years ago

I'd be open to a PR, although @xingjiepan knows more about that benchmark than I do.

spiderbaby commented 7 years ago

Amelie put together some great notes on the Kortemme Lab wiki about the dataset - they should probably be included in some form in the repository since they are currently unavailable to most people. Maybe loop (harhar) her into the conversation if she's not already on the list? I'm on my phone so I can't check her email address easily.

On Aug 21, 2017, at 7:16 PM, Kale Kundert notifications@github.com wrote:

I'd be open to a PR, although @xingjiepan knows more about that benchmark than I do.

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smlewis commented 7 years ago

In my local version I did it by sed -i 's/HETATM/REMARK/' *pdb in the 14-17 directory that was interesting to me - this lets Rosetta handle it but also leaves the core data there if you decide you want it later. I leave the decision on whether you want it in your hands; and will set up the PR if you do.

@spiderbaby - send me an email so I have a working address; the only email address I have for you is dead. (the public github one included).

spiderbaby commented 7 years ago

Nearly there, just put @gmail.com onto the end of spiderbaby. I'll check that public GitHub address later, thanks for the heads-up.

On Aug 22, 2017, at 8:11 AM, Steven Lewis notifications@github.com wrote:

In my local version I did it by sed -i 's/HETATM/REMARK/' *pdb in the 14-17 directory that was interesting to me - this lets Rosetta handle it but also leaves the core data there if you decide you want it later. I leave the decision on whether you want it in your hands; and will set up the PR if you do.

@spiderbaby - send me an email so I have a working address; the only email address I have for you is dead. (the public github one included).

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

amelie-stein commented 7 years ago

The comments Shane mentioned are in the Kortemme lab wiki, so I can't access them anymore, but some of you should be able to. I'm happy to revise and elaborate if anything is unclear.